[English] 日本語
Yorodumi
- PDB-1m78: CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH DIHYDRO-N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m78
TitleCANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NADPH) AND 5-CHLORYL-2,4,6-QUINAZOLINETRIAMINE (GW1225)
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / ANTIFUNGAL TARGET / REDUCTASE
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-CHLORYL-2,4,6-QUINAZOLINETRIAMINE / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / DIRECT REPLACEMENT / Resolution: 1.71 Å
AuthorsWhitlow, M. / Howard, A.J. / Kuyper, L.F.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: X-Ray Crystallographic Studies of Candida Albicans Dihydrofolate Reductase. High Resolution Structures of the Holoenzyme and an Inhibited Ternary Complex.
Authors: Whitlow, M. / Howard, A.J. / Stewart, D. / Hardman, K.D. / Kuyper, L.F. / Baccanari, D.P. / Fling, M.E. / Tansik, R.L.
#1: Journal: J.Med.Chem. / Year: 2001
Title: X-Ray Crystal Structures of Candida Albicans Dihydrofolate Reductase: High Resolution Ternary Complexes in which the Dihydronicotinamide Moiety of Nadph is Displaced by an Inhibitor
Authors: Whitlow, M. / Howard, A.J. / Stewart, D. / Hardman, K.D. / Chan, J.H. / Baccanari, D.P. / Tansik, R.L. / Hong, J.S. / Kuyper, L.F.
#2: Journal: J.Med.Chem. / Year: 1995
Title: Selective Inhibitors of Candida Albicans Dihydrofolate Reductase: Activity and Selectivity of 5-(Arylthio)-2,4-Diaminoquinazolines
Authors: Chan, J.H. / Hong, J.S. / Kuyper, L.F. / Baccanari, D.P. / Joyner, S.S. / Tansik, R.L. / Boytos, C.M. / Rudolph, S.K.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Characterization of Candida Albicans Dihydrofolate Reductase
Authors: Baccanari, D.P. / Tansik, R.L. / Joyner, S.S. / Fling, M.E. / Smith, P.L. / Freisheim, J.H.
History
DepositionJul 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2996
Polymers44,3892
Non-polymers1,9104
Water6,071337
1
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1503
Polymers22,1951
Non-polymers9552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1503
Polymers22,1951
Non-polymers9552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.910, 67.280, 38.490
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDihydrofolate reductase is active as a monomer.

-
Components

#1: Protein DIHYDROFOLATE REDUCTASE / DHFR


Mass: 22194.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: DFR1 / Plasmid: P1869 / Species (production host): Escherichia coli / Cellular location (production host): cytoplasm / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22906, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-CLZ / 5-CHLORYL-2,4,6-QUINAZOLINETRIAMINE


Mass: 209.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8ClN5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / Method: liquid diffusion / pH: 7.5
Details: dihydro-nicotinamide-adenine-dinucleotide phosphate (NADPH), 5-chloryl-2,4,6-quinazolinetriamine (GW1225), PEG-3350, Potassium 4-morphilineethanesulfonic acid (MES), dithiothreitol (DTT), pH ...Details: dihydro-nicotinamide-adenine-dinucleotide phosphate (NADPH), 5-chloryl-2,4,6-quinazolinetriamine (GW1225), PEG-3350, Potassium 4-morphilineethanesulfonic acid (MES), dithiothreitol (DTT), pH 7.50, LIQUID DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Mar 29, 1988 / Details: Huber graphite MONOCHROMATOR
RadiationMonochromator: HUBER GRAPHITE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 37244 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.118 % / Biso Wilson estimate: 34.35 Å2 / Rmerge(I) obs: 0.0537 / Rsym value: 0.0537 / Net I/σ(I): 17.6
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.2337 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4052 / Rsym value: 0.2337 / % possible all: 60.55

-
Processing

Software
NameClassification
X-GENdata reduction
FRODOmodel building
PROFFTrefinement
X-GENdata scaling
RefinementMethod to determine structure: DIRECT REPLACEMENT
Starting model: CANDIDA ALBICANS DHFR (PDB ENTRY 1AI9)

1ai9


Resolution: 1.71→10 Å
Isotropic thermal model: Konnert, J.H. & Hendrickson, W.A. (1980) Acta Crystallogr. A A36, 344.
σ(F): 2 / σ(I): -3
Stereochemistry target values: Hendrickson, W.A. (1985) Methods Enzymol. 115, 252-270.
RfactorNum. reflection% reflection
Rwork0.1557 --
all0.1557 37249 -
obs0.1557 32743 91.5 %
Refinement stepCycle: LAST / Resolution: 1.71→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 124 348 3654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.03
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1
X-RAY DIFFRACTIONp_mcbond_it4.6281
X-RAY DIFFRACTIONp_mcangle_it5.2072
X-RAY DIFFRACTIONp_scbond_it6.1192.5
X-RAY DIFFRACTIONp_scangle_it7.6125
X-RAY DIFFRACTIONp_plane_restr0.0190.03
X-RAY DIFFRACTIONp_chiral_restr0.2470.3
X-RAY DIFFRACTIONp_singtor_nbd0.1640.2
X-RAY DIFFRACTIONp_multtor_nbd0.1450.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2
X-RAY DIFFRACTIONp_xyhbond_nbd0.1450.2
X-RAY DIFFRACTIONp_planar_tor3.76
X-RAY DIFFRACTIONp_staggered_tor14.710
X-RAY DIFFRACTIONp_transverse_tor30.810
X-RAY DIFFRACTIONp_special_tor6
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
1.71-1.850.203X-RAY DIFFRACTION2794
1.85-20.171X-RAY DIFFRACTION5131
2-2.250.159X-RAY DIFFRACTION6930
2.25-2.70.159X-RAY DIFFRACTION7409
2.7-3.40.147X-RAY DIFFRACTION5266
3.4-100.147X-RAY DIFFRACTION5213

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more